Genomic and transcriptomic analysis in the Antarctic ciliate Euplotes focardii: insights regarding the evolution of the molecular basis of cold adaptation

Ciliates provide optimal model systems to study environmental adaptation. Comparative transcriptomic analysis of Euplotes focardii, a strictly psychrophilic ciliate isolated from Antarctic seawater, and the mesophilic congeneric species E. crassus revealed that in E. focardii the majority of the expressed genes code for proteins involved in oxidoreductase activity, as reported for Antarctic fishes and krill. These results confirm that a major problem of Antarctic marine organisms is to cope with increased O2 solubility at low temperatures. They also suggest that an increased defence against oxidative stress likely provides an important evolutionary feature that allowed the adaptation of Antarctic organisms in their oxygen-rich environment. Quantitative PCR showed that expression of Hsp70 genes was induced when E. focardii cells were subjected to oxidative stress, whereas thermal stress did not cause induction. These results argue that E. focardii in its current environment is well protected against reactive oxygen species and are consistent with prior reports of constitutive Hsp70 expression as a defence against cold-induced protein denaturation. E. focardii appears to be poised to cope with the oxidative challenge that is likely to accompany oceanic warming over the next century, but the absence of a temperature-inducible chaperone response may place its proteome at risk. E. focardii genome sequences reported by Lobanov et al. (2017) have been re-assembled by SPAdes with a 25% improvement in the number of contigs, with about 25000 nanochromosomes identified and annotated. Gene families involved in oxidative stress appeared significantly expanded in paralogous genes in E. focardii with respect to E. crassus and E. octocarinatus, thus suggesting gene duplication as mechanism at the basis of molecular cold adaptation. The comparative genome analysis of Euplotes species also revealed a rapid evolution and unusual plasticity of the programmed ribosomal frameshifting, a process that allows the change of the reading frame during translation. This process appears pervasive in Euplotes and it is not conserved in the affected genes of the different species. Attempts were performed to annotate all the genes subjected to frameshifting in E. focardii and unusual sites for +2 frameshifting were found.